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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 443 by mmeineke, Wed Apr 2 22:19:03 2003 UTC vs.
Revision 690 by mmeineke, Tue Aug 12 21:44:06 2003 UTC

# Line 1 | Line 1
1   #include <cstdlib>
2   #include <cstring>
3 + #include <cmath>
4  
5 + #include <iostream>
6 + using namespace std;
7  
8   #include "SimInfo.hpp"
9   #define __C
# Line 9 | Line 12 | SimInfo* currentInfo;
12  
13   #include "fortranWrappers.hpp"
14  
15 + #ifdef IS_MPI
16 + #include "mpiSimulation.hpp"
17 + #endif
18 +
19 + inline double roundMe( double x ){
20 +  return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 );
21 + }
22 +          
23 +
24   SimInfo* currentInfo;
25  
26   SimInfo::SimInfo(){
# Line 16 | Line 28 | SimInfo::SimInfo(){
28    n_constraints = 0;
29    n_oriented = 0;
30    n_dipoles = 0;
31 +  ndf = 0;
32 +  ndfRaw = 0;
33 +  nZconstraints = 0;
34    the_integrator = NULL;
35    setTemp = 0;
36    thermalTime = 0.0;
37 +  currentTime = 0.0;
38    rCut = 0.0;
39 +  origRcut = -1.0;
40 +  ecr = 0.0;
41 +  origEcr = -1.0;
42 +  est = 0.0;
43 +  oldEcr = 0.0;
44 +  oldRcut = 0.0;
45  
46 +  haveOrigRcut = 0;
47 +  haveOrigEcr = 0;
48 +  boxIsInit = 0;
49 +  
50 +  
51 +
52    usePBC = 0;
53    useLJ = 0;
54    useSticky = 0;
# Line 29 | Line 57 | SimInfo::SimInfo(){
57    useGB = 0;
58    useEAM = 0;
59  
60 +  myConfiguration = new SimState();
61  
33 –
62    wrapMeSimInfo( this );
63 + }
64 +
65 +
66 + SimInfo::~SimInfo(){
67 +
68 +  delete myConfiguration;
69 +
70 +  map<string, GenericData*>::iterator i;
71 +  
72 +  for(i = properties.begin(); i != properties.end(); i++)
73 +    delete (*i).second;
74 +    
75 + }
76 +
77 + void SimInfo::setBox(double newBox[3]) {
78 +  
79 +  int i, j;
80 +  double tempMat[3][3];
81 +
82 +  for(i=0; i<3; i++)
83 +    for (j=0; j<3; j++) tempMat[i][j] = 0.0;;
84 +
85 +  tempMat[0][0] = newBox[0];
86 +  tempMat[1][1] = newBox[1];
87 +  tempMat[2][2] = newBox[2];
88 +
89 +  setBoxM( tempMat );
90 +
91 + }
92 +
93 + void SimInfo::setBoxM( double theBox[3][3] ){
94 +  
95 +  int i, j, status;
96 +  double smallestBoxL, maxCutoff;
97 +  double FortranHmat[9]; // to preserve compatibility with Fortran the
98 +                         // ordering in the array is as follows:
99 +                         // [ 0 3 6 ]
100 +                         // [ 1 4 7 ]
101 +                         // [ 2 5 8 ]
102 +  double FortranHmatInv[9]; // the inverted Hmat (for Fortran);
103 +
104 +  
105 +  if( !boxIsInit ) boxIsInit = 1;
106 +
107 +  for(i=0; i < 3; i++)
108 +    for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j];
109 +  
110 +  calcBoxL();
111 +  calcHmatInv();
112 +
113 +  for(i=0; i < 3; i++) {
114 +    for (j=0; j < 3; j++) {
115 +      FortranHmat[3*j + i] = Hmat[i][j];
116 +      FortranHmatInv[3*j + i] = HmatInv[i][j];
117 +    }
118 +  }
119 +
120 +  setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic);
121 +
122 + }
123 +
124 +
125 + void SimInfo::getBoxM (double theBox[3][3]) {
126 +
127 +  int i, j;
128 +  for(i=0; i<3; i++)
129 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j];
130 + }
131 +
132 +
133 + void SimInfo::scaleBox(double scale) {
134 +  double theBox[3][3];
135 +  int i, j;
136 +
137 +  // cerr << "Scaling box by " << scale << "\n";
138 +
139 +  for(i=0; i<3; i++)
140 +    for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale;
141 +
142 +  setBoxM(theBox);
143 +
144 + }
145 +
146 + void SimInfo::calcHmatInv( void ) {
147 +  
148 +  int i,j;
149 +  double smallDiag;
150 +  double tol;
151 +  double sanity[3][3];
152 +
153 +  invertMat3( Hmat, HmatInv );
154 +
155 +  // Check the inverse to make sure it is sane:
156 +
157 +  matMul3( Hmat, HmatInv, sanity );
158 +    
159 +  // check to see if Hmat is orthorhombic
160 +  
161 +  smallDiag = Hmat[0][0];
162 +  if(smallDiag > Hmat[1][1]) smallDiag = Hmat[1][1];
163 +  if(smallDiag > Hmat[2][2]) smallDiag = Hmat[2][2];
164 +  tol = smallDiag * 1E-6;
165 +
166 +  orthoRhombic = 1;
167 +  
168 +  for (i = 0; i < 3; i++ ) {
169 +    for (j = 0 ; j < 3; j++) {
170 +      if (i != j) {
171 +        if (orthoRhombic) {
172 +          if (Hmat[i][j] >= tol) orthoRhombic = 0;
173 +        }        
174 +      }
175 +    }
176 +  }
177 + }
178 +
179 + double SimInfo::matDet3(double a[3][3]) {
180 +  int i, j, k;
181 +  double determinant;
182 +
183 +  determinant = 0.0;
184 +
185 +  for(i = 0; i < 3; i++) {
186 +    j = (i+1)%3;
187 +    k = (i+2)%3;
188 +
189 +    determinant += a[0][i] * (a[1][j]*a[2][k] - a[1][k]*a[2][j]);
190 +  }
191 +
192 +  return determinant;
193 + }
194 +
195 + void SimInfo::invertMat3(double a[3][3], double b[3][3]) {
196 +  
197 +  int  i, j, k, l, m, n;
198 +  double determinant;
199 +
200 +  determinant = matDet3( a );
201 +
202 +  if (determinant == 0.0) {
203 +    sprintf( painCave.errMsg,
204 +             "Can't invert a matrix with a zero determinant!\n");
205 +    painCave.isFatal = 1;
206 +    simError();
207 +  }
208 +
209 +  for (i=0; i < 3; i++) {
210 +    j = (i+1)%3;
211 +    k = (i+2)%3;
212 +    for(l = 0; l < 3; l++) {
213 +      m = (l+1)%3;
214 +      n = (l+2)%3;
215 +      
216 +      b[l][i] = (a[j][m]*a[k][n] - a[j][n]*a[k][m]) / determinant;
217 +    }
218 +  }
219 + }
220 +
221 + void SimInfo::matMul3(double a[3][3], double b[3][3], double c[3][3]) {
222 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
223 +
224 +  r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
225 +  r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
226 +  r02 = a[0][0]*b[0][2] + a[0][1]*b[1][2] + a[0][2]*b[2][2];
227 +  
228 +  r10 = a[1][0]*b[0][0] + a[1][1]*b[1][0] + a[1][2]*b[2][0];
229 +  r11 = a[1][0]*b[0][1] + a[1][1]*b[1][1] + a[1][2]*b[2][1];
230 +  r12 = a[1][0]*b[0][2] + a[1][1]*b[1][2] + a[1][2]*b[2][2];
231 +  
232 +  r20 = a[2][0]*b[0][0] + a[2][1]*b[1][0] + a[2][2]*b[2][0];
233 +  r21 = a[2][0]*b[0][1] + a[2][1]*b[1][1] + a[2][2]*b[2][1];
234 +  r22 = a[2][0]*b[0][2] + a[2][1]*b[1][2] + a[2][2]*b[2][2];
235 +  
236 +  c[0][0] = r00; c[0][1] = r01; c[0][2] = r02;
237 +  c[1][0] = r10; c[1][1] = r11; c[1][2] = r12;
238 +  c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
239 + }
240 +
241 + void SimInfo::matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
242 +  double a0, a1, a2;
243 +
244 +  a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
245 +
246 +  outVec[0] = m[0][0]*a0 + m[0][1]*a1 + m[0][2]*a2;
247 +  outVec[1] = m[1][0]*a0 + m[1][1]*a1 + m[1][2]*a2;
248 +  outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
249 + }
250 +
251 + void SimInfo::transposeMat3(double in[3][3], double out[3][3]) {
252 +  double temp[3][3];
253 +  int i, j;
254 +
255 +  for (i = 0; i < 3; i++) {
256 +    for (j = 0; j < 3; j++) {
257 +      temp[j][i] = in[i][j];
258 +    }
259 +  }
260 +  for (i = 0; i < 3; i++) {
261 +    for (j = 0; j < 3; j++) {
262 +      out[i][j] = temp[i][j];
263 +    }
264 +  }
265 + }
266 +  
267 + void SimInfo::printMat3(double A[3][3] ){
268 +
269 +  std::cerr
270 +            << "[ " << A[0][0] << ", " << A[0][1] << ", " << A[0][2] << " ]\n"
271 +            << "[ " << A[1][0] << ", " << A[1][1] << ", " << A[1][2] << " ]\n"
272 +            << "[ " << A[2][0] << ", " << A[2][1] << ", " << A[2][2] << " ]\n";
273 + }
274 +
275 + void SimInfo::printMat9(double A[9] ){
276 +
277 +  std::cerr
278 +            << "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n"
279 +            << "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n"
280 +            << "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n";
281 + }
282 +
283 + void SimInfo::calcBoxL( void ){
284 +
285 +  double dx, dy, dz, dsq;
286 +  int i;
287 +
288 +  // boxVol = Determinant of Hmat
289 +
290 +  boxVol = matDet3( Hmat );
291 +
292 +  // boxLx
293 +  
294 +  dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0];
295 +  dsq = dx*dx + dy*dy + dz*dz;
296 +  boxL[0] = sqrt( dsq );
297 +  maxCutoff = 0.5 * boxL[0];
298 +
299 +  // boxLy
300 +  
301 +  dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1];
302 +  dsq = dx*dx + dy*dy + dz*dz;
303 +  boxL[1] = sqrt( dsq );
304 +  if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1];
305 +
306 +  // boxLz
307 +  
308 +  dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2];
309 +  dsq = dx*dx + dy*dy + dz*dz;
310 +  boxL[2] = sqrt( dsq );
311 +  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
312 +  
313 +  checkCutOffs();
314 +
315   }
316  
317 +
318 + void SimInfo::wrapVector( double thePos[3] ){
319 +
320 +  int i, j, k;
321 +  double scaled[3];
322 +
323 +  if( !orthoRhombic ){
324 +    // calc the scaled coordinates.
325 +  
326 +
327 +    matVecMul3(HmatInv, thePos, scaled);
328 +    
329 +    for(i=0; i<3; i++)
330 +      scaled[i] -= roundMe(scaled[i]);
331 +    
332 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
333 +    
334 +    matVecMul3(Hmat, scaled, thePos);
335 +
336 +  }
337 +  else{
338 +    // calc the scaled coordinates.
339 +    
340 +    for(i=0; i<3; i++)
341 +      scaled[i] = thePos[i]*HmatInv[i][i];
342 +    
343 +    // wrap the scaled coordinates
344 +    
345 +    for(i=0; i<3; i++)
346 +      scaled[i] -= roundMe(scaled[i]);
347 +    
348 +    // calc the wrapped real coordinates from the wrapped scaled coordinates
349 +    
350 +    for(i=0; i<3; i++)
351 +      thePos[i] = scaled[i]*Hmat[i][i];
352 +  }
353 +    
354 + }
355 +
356 +
357 + int SimInfo::getNDF(){
358 +  int ndf_local, ndf;
359 +  
360 +  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
361 +
362 + #ifdef IS_MPI
363 +  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
364 + #else
365 +  ndf = ndf_local;
366 + #endif
367 +
368 +  ndf = ndf - 3 - nZconstraints;
369 +
370 +  return ndf;
371 + }
372 +
373 + int SimInfo::getNDFraw() {
374 +  int ndfRaw_local, ndfRaw;
375 +
376 +  // Raw degrees of freedom that we have to set
377 +  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
378 +  
379 + #ifdef IS_MPI
380 +  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
381 + #else
382 +  ndfRaw = ndfRaw_local;
383 + #endif
384 +
385 +  return ndfRaw;
386 + }
387 +
388   void SimInfo::refreshSim(){
389  
390    simtype fInfo;
391    int isError;
392 +  int n_global;
393    int* excl;
394  
395 <  fInfo.box[0] = box_x;
44 <  fInfo.box[1] = box_y;
45 <  fInfo.box[2] = box_z;
395 >  fInfo.dielect = 0.0;
396  
397 <  fInfo.rlist = rList;
398 <  fInfo.rcut = rCut;
399 <  fInfo.rrf = ecr;
50 <  fInfo.rt = ecr - est;
51 <  fInfo.dielect = dielectric;
397 >  if( useDipole ){
398 >    if( useReactionField )fInfo.dielect = dielectric;
399 >  }
400  
401    fInfo.SIM_uses_PBC = usePBC;
402    //fInfo.SIM_uses_LJ = 0;
# Line 64 | Line 412 | void SimInfo::refreshSim(){
412  
413    excl = Exclude::getArray();
414  
415 + #ifdef IS_MPI
416 +  n_global = mpiSim->getTotAtoms();
417 + #else
418 +  n_global = n_atoms;
419 + #endif
420 +
421    isError = 0;
422  
423 < //   fInfo;
424 < //   n_atoms;
425 < //   identArray;
72 < //   n_exclude;
73 < //   excludes;
74 < //   nGlobalExcludes;
75 < //   globalExcludes;
76 < //   isError;
423 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
424 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
425 >                  &isError );
426  
78 –  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl,
79 –                  &nGlobalExcludes, globalExcludes, &isError );
80 –
427    if( isError ){
428  
429      sprintf( painCave.errMsg,
# Line 91 | Line 437 | void SimInfo::refreshSim(){
437             "succesfully sent the simulation information to fortran.\n");
438    MPIcheckPoint();
439   #endif // is_mpi
440 +
441 +  this->ndf = this->getNDF();
442 +  this->ndfRaw = this->getNDFraw();
443 +
444   }
445  
446 +
447 + void SimInfo::setRcut( double theRcut ){
448 +
449 +  if( !haveOrigRcut ){
450 +    haveOrigRcut = 1;
451 +    origRcut = theRcut;
452 +  }
453 +
454 +  rCut = theRcut;
455 +  checkCutOffs();
456 + }
457 +
458 + void SimInfo::setEcr( double theEcr ){
459 +
460 +  if( !haveOrigEcr ){
461 +    haveOrigEcr = 1;
462 +    origEcr = theEcr;
463 +  }
464 +
465 +  ecr = theEcr;
466 +  checkCutOffs();
467 + }
468 +
469 + void SimInfo::setEcr( double theEcr, double theEst ){
470 +
471 +  est = theEst;
472 +  setEcr( theEcr );
473 + }
474 +
475 +
476 + void SimInfo::checkCutOffs( void ){
477 +
478 +  int cutChanged = 0;
479 +
480 +
481 +
482 +  if( boxIsInit ){
483 +    
484 +    //we need to check cutOffs against the box
485 +  
486 +    if(( maxCutoff > rCut )&&(usePBC)){
487 +      if( rCut < origRcut ){
488 +        rCut = origRcut;
489 +        if (rCut > maxCutoff) rCut = maxCutoff;
490 +        
491 +        sprintf( painCave.errMsg,
492 +                 "New Box size is setting the long range cutoff radius "
493 +                 "to %lf\n",
494 +                 rCut );
495 +        painCave.isFatal = 0;
496 +        simError();
497 +      }
498 +    }
499 +
500 +    if( maxCutoff > ecr ){
501 +      if( ecr < origEcr ){
502 +        rCut = origEcr;
503 +        if (ecr > maxCutoff) ecr = maxCutoff;
504 +        
505 +        sprintf( painCave.errMsg,
506 +                 "New Box size is setting the electrostaticCutoffRadius "
507 +                 "to %lf\n",
508 +                 ecr );
509 +        painCave.isFatal = 0;
510 +        simError();
511 +      }
512 +    }
513 +
514 +
515 +    if ((rCut > maxCutoff)&&(usePBC)) {
516 +      sprintf( painCave.errMsg,
517 +               "New Box size is setting the long range cutoff radius "
518 +               "to %lf\n",
519 +               maxCutoff );
520 +      painCave.isFatal = 0;
521 +      simError();
522 +      rCut = maxCutoff;
523 +    }
524 +
525 +    if( ecr > maxCutoff){
526 +      sprintf( painCave.errMsg,
527 +               "New Box size is setting the electrostaticCutoffRadius "
528 +               "to %lf\n",
529 +               maxCutoff  );
530 +      painCave.isFatal = 0;
531 +      simError();      
532 +      ecr = maxCutoff;
533 +    }
534 +
535 +    
536 +  }
537 +  
538 +
539 +  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
540 +
541 +  // rlist is the 1.0 plus max( rcut, ecr )
542 +  
543 +  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
544 +
545 +  if( cutChanged ){
546 +    
547 +    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
548 +  }
549 +
550 +  oldEcr = ecr;
551 +  oldRcut = rCut;
552 + }
553 +
554 + void SimInfo::addProperty(GenericData* prop){
555 +
556 +  map<string, GenericData*>::iterator result;
557 +  result = properties.find(prop->getID());
558 +  
559 +  //we can't simply use  properties[prop->getID()] = prop,
560 +  //it will cause memory leak if we already contain a propery which has the same name of prop
561 +  
562 +  if(result != properties.end()){
563 +    
564 +    delete (*result).second;
565 +    (*result).second = prop;
566 +      
567 +  }
568 +  else{
569 +
570 +    properties[prop->getID()] = prop;
571 +
572 +  }
573 +    
574 + }
575 +
576 + GenericData* SimInfo::getProperty(const string& propName){
577 +
578 +  map<string, GenericData*>::iterator result;
579 +  
580 +  //string lowerCaseName = ();
581 +  
582 +  result = properties.find(propName);
583 +  
584 +  if(result != properties.end())
585 +    return (*result).second;  
586 +  else  
587 +    return NULL;  
588 + }
589 +
590 + vector<GenericData*> SimInfo::getProperties(){
591 +
592 +  vector<GenericData*> result;
593 +  map<string, GenericData*>::iterator i;
594 +  
595 +  for(i = properties.begin(); i != properties.end(); i++)
596 +    result.push_back((*i).second);
597 +    
598 +  return result;
599 + }
600 +
601 +

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